Ira Steven Behr ordered this episode because he felt that they needed to close off some of the dangling story threads before moving into the Dominion war story. In fact his preference was to obliterate the entire Maquis in this episode, ending that entire story once and for all. Rick Berman wouldn't allow this, as he felt that Voyager might want to use the Maquis at some point. Deep Space Nine would never mention the Maquis again, however, and ironically when Voyager did reference the Maquis back home, it would be B'Elanna telling Chakotay that the organisation had been all but destroyed by the Dominion.

A mention by Sisko of a recent Borg attack places Star Trek : First Contact as happening shortly before this episode.

Plotline

A message to Maquis leader Eddington indicates that a flotilla of cloaked missiles are on their way to wipe out Cardassia in reprisal for the Jem'Hadars virtual annhilation of the terrorist group. Sisko must pair up with his former enemy to stop the missiles before the Jem'Hadar go on the rampage in response - but as always, Eddington has his own agenda.